A. Project Summary/Abstract Recoding describes the local reprogramming of mRNA translation to discard standard translational rules and decode non-canonically. The products of this stimulated process, proteins incorporating shifts in reading frame, bypassed nucleotide segments, and/or unexpected amino acids have been observed in all 3 domains and are known to contribute importantly to post-transcriptional regulation of gene expression. Our hypothesis is that recoded and miscoded proteins are more important than previously anticipated, but that they are consistently overlooked by high-throughput proteomic methods that regard the proteome as a mirror of the genome. We believe that an altered proteomic workflow can reveal proteins recoded and miscoded in vivo, and that these methods can provide amino acid sequences for some of the recoded products. If successful, these efforts can potentially impact research in protein translation, microbiology, and proteomics. They can impact the development of therapies for genetic diseases, and can suggest explanations for the unusual activity differences observed for some gene products differing only by a synonymous polymorphism. They may also suggest a function for pseudo-messenger RNA. B. Project Narrative This proposal describes a method to examine the importance of an alternate pathway for synthesizing essential components of life. Should the pathway be found to be more important than previously anticipated, it will suggest causes and potential therapies for some disorders.